Method of generating interacting peptides

Abstract

Disclosed herein is a method of designing small peptides for interacting with, binding to, or modulating the activity of, known protein or peptides. Further disclosed herein are methods for selecting sequences likely to have high binding activity against known protein sequences as well as peptides derived from the disclosed methods.

1 . A composition comprising a binding polypeptide configured to interact with a known binding partner wherein said binding polypeptide has a sequence of between 6 and 30 amino acids in length; and
 wherein said binding polypeptide sequence is composed by the steps of identifying the sequence of said binding partner; and, identifying 20% or more of the residues in said binding partner sequence; and, for each of the identified residues within the binding partner sequence, selecting the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence as follows:   where the identified residue within the binding partner sequence is Phe, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Lys or Glu;   where the identified residue within the binding partner sequence is Leu, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Gln, Lys, or Glu;   where the identified residue within the binding partner sequence is Ser, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Arg, Gly, Thr, or Ala;   where the identified residue within the binding partner sequence is Thr, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ser, Gly, Cys, or Arg;   where the identified residue within the binding partner sequence is Tyr, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ile or Val;   where the identified residue within the binding partner sequence is Cys, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Thr or Ala;   where the identified residue within the binding partner sequence is Trp, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Pro;   where the identified residue within the binding partner sequence is Ile, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Asn, Asp, or Tyr;   where the identified residue within the binding partner sequence is Met, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is His;   where the identified residue within the binding partner sequence is Asn, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ile or Val;   where the identified residue within the binding partner sequence is Lys, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Phe or Leu;   where the identified residue within the binding partner sequence is Arg, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Thr, Ala, Ser, or Pro;   where the identified residue within the binding partner sequence is Pro, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Arg, Gly, or Trp;   where the identified residue within the binding partner sequence is His, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Met or Val;   where the identified residue within the binding partner sequence is Gln, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Leu;   where the identified residue within the binding partner sequence is Val, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Asn, Asp, Tyr, or His;   where the identified residue within the binding partner sequence is Ala, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ser, Gly, Cys, or Arg;   where the identified residue within the binding partner sequence is Asp, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ile or Val;   where the identified residue within the binding partner sequence is Glu, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Phe or Leu;   where the identified residue within the binding partner sequence is Gly, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Thr, Ala, Ser, or Pro;   
       and wherein said binding polypeptide may comprise part of a larger polypeptide. 
     
     
         2 . A method of making a polypeptide configured to interact with a known binding partner wherein said binding polypeptide has a sequence of between 6 and 20 amino acids in length; and
 wherein said binding polypeptide sequence is assembled by the steps of:   identifying the sequence of said binding partner; and, identifying 20% or more of the residues in said binding partner sequence; and, for each of the identified residues within the binding partner sequence, selecting the corresponding residue for inclusion in the sequence of said binding polypeptide sequence as follows:   where the identified residue within the binding partner sequence is Phe, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Lys or Glu;   where the identified residue within the binding partner sequence is Leu, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Gln, Lys, or Glu;   where the identified residue within the binding partner sequence is Ser, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Arg, Gly, Thr, or Ala;   where the identified residue within the binding partner sequence is Thr, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ser, Gly, Cys, or Arg;   where the identified residue within the binding partner sequence is Tyr, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ile or Val;   where the identified residue within the binding partner sequence is Cys, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Thr or Ala;   where the identified residue within the binding partner sequence is Trp, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Pro;   where the identified residue within the binding partner sequence is Ile, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Asn, Asp, or Tyr;   where the identified residue within the binding partner sequence is Met, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is His;   where the identified residue within the binding partner sequence is Asn, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ile or Val;   where the identified residue within the binding partner sequence is Lys, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Phe or Leu;   where the identified residue within the binding partner sequence is Arg, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Thr, Ala, Ser, or Pro;   where the identified residue within the binding partner sequence is Pro, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Arg, Gly, or Trp;   where the identified residue within the binding partner sequence is His, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Met or Val;   where the identified residue within the binding partner sequence is Gln, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Leu;   where the identified residue within the binding partner sequence is Val, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Asn, Asp, Tyr, or His;   where the identified residue within the binding partner sequence is Ala, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ser, Gly, Cys, or Arg;   where the identified residue within the binding partner sequence is Asp, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Ile or Val;   where the identified residue within the binding partner sequence is Glu, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Phe or Leu;   where the identified residue within the binding partner sequence is Gly, the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence is Thr, Ala, Ser, or Pro;   and wherein said binding polypeptide may comprise part of a larger polypeptide.   
     
     
         3 . (canceled) 
     
     
         4 . (canceled) 
     
     
         5 . (canceled) 
     
     
         6 . (canceled) 
     
     
         7 . (canceled) 
     
     
         8 . The composition of  claim 1 , wherein the selected corresponding residues for inclusion in the binding polypeptide sequence occur at one of every two positions in the binding polypeptide sequence. 
     
     
         9 . The composition of  claim 1 , wherein the selected corresponding residues for inclusion in the binding polypeptide sequence occur at every other position in the binding polypeptide sequence. 
     
     
         10 . The composition of  claim 1 , wherein the selected corresponding residues for inclusion in the binding polypeptide sequence occur at one of every three positions in the binding polypeptide sequence. 
     
     
         11 . The composition of  claim 1 , wherein the selected corresponding residues for inclusion in the binding polypeptide sequence occur at every third position in the binding polypeptide sequence. 
     
     
         12 . The composition of  claim 1 , wherein the selected corresponding residues for inclusion in the binding polypeptide sequence occur at two of every three positions in the binding polypeptide sequence. 
     
     
         13 . A polypeptide made according to the method of  claim 2 . 
     
     
         14 . The polypeptide of  claim 1 , further comprising a functional moiety. 
     
     
         15 . The polypeptide of  claim 14  wherein said functional moiety comprises one or more of a polypeptide, a therapeutic molecule, a protein, a nucleic acid, or a diagnostic moiety. 
     
     
         16 . The polypeptide of  claim 14  wherein said functional moiety comprises one or more of a radiolabel, spin label, affinity tag, or fluorescent label. 
     
     
         17 . The polypeptide of  claim 14  further comprising a linker. 
     
     
         18 . (canceled) 
     
     
         19 . The polypeptide of  claim 17  wherein said peptide has the sequence GSGS (SEQ ID NO: 1), (G) n  (SEQ ID NO: 2), (GS) n  (SEQ ID NO: 3), (GGSGG) n  (SEQ ID NO: 4), (GGGS) n  (SEQ ID NO: 5), CYPEN (SEQ ID NO: 6), or KTGEVNN (SEQ ID NO: 7). 
     
     
         20 . A binding polypeptide according to  claim 1 , wherein said binding polypeptide contains residues configured to interact with a second and optionally a third target protein in addition to the first target protein. 
     
     
         21 . A binding polypeptide generated according to  claim 2 , wherein said binding polypeptide contains residues configured to interact with a second and optionally a third target protein in addition to the first target protein. 
     
     
         22 . A fusion polypeptide, wherein said fusion comprises one or more binding polypeptides made according to the method of  claim 2 . 
     
     
         23 . (canceled) 
     
     
         24 . The composition of  claim 1 , wherein said binding polypeptide is incorporated within a fusion polypeptide, and wherein said fusion comprises may further comprise one or more additional binding polypeptides. 
     
     
         25 . (canceled) 
     
     
         26 . A binding polypeptide according to  claim 1 , wherein the sequence of said polypeptide comprises one or more of sequence LEQIKRLF (SEQ ID NO: 8), LLQVDVILL (SEQ ID NO: 9), LLQVDVILLCYPENLEQIKIRLF (SEQ ID NO: 10), LLQVDVILLCYPENLEQIKIRLFGSGSHHHHHH (SEQ ID NO: 11), EDRLQSYDLD (SEQ ID NO: 12), EDRLQSYDLDGSGSHHHHHH (SEQ ID NO: 13), ELDKAGFIKRQL (SEQ ID NO: 14), LEERGVKDRQLQ (SEQ ID NO: 15), LEILRAKDLALE (SEQ ID NO: 16), LEQIKIRLF (SEQ ID NO: 17), LSGLNEQRTQ (SEQ ID NO: 18), YDVDAIVPQC (SEQ ID NO: 19), CLTYDSHYLQ (SEQ ID NO: 20), LVAHVTSRKC (SEQ ID NO: 21), EYRLYLRALC (SEQ ID NO: 22), IEIVRKKPIF (SEQ ID NO: 23), IEIVRKKPIFC (SEQ ID NO: 24), CEDRLQSYDLD (SEQ ID NO: 25), EKLYLYYLQ (SEQ ID NO: 26), EKLYLYYLQC (SEQ ID NO: 27), LEQIKIRLFGSGSHHHHHH (SEQ ID NO: 28), LSRAYLSYEGSGSHHHHHH (SEQ ID NO: 29), EYRLYLRALCYPENLSRAYLSYEGSGSHHHHHH (SEQ ID NO: 30), DLDYAQLRDKCYPENEDRLQSYDLDGSGSHHHHHH (SEQ ID NO: 31), GKPIPNPLLGLDST (SEQ ID NO: 32), ELDKAGFIKRQLC (SEQ ID NO: 33), LLQVDVILLHHHHHHLEQIKIRLF (SEQ ID NO: 34), and/or CFFDSLVKQ (SEQ ID NO: 35). 
     
     
         27 . A binding polypeptide according to  claim 1 , or a nucleic acid encoding said binding peptide, wherein the sequence of said polypeptide comprises one or more of the sequences provided in Table 6 or 7. 
     
     
         28 . (canceled) 
     
     
         29 . A method of making a binding polypeptide configured to interact with a known binding partner wherein said binding polypeptide has a sequence of between 6 and 30 amino acids in length; and
 wherein said binding polypeptide sequence is composed by the steps of identifying the sequence of said binding partner; and, identifying 20% or more of the residues in said binding partner sequence; and,   for each of the identified residues within the binding partner sequence, selecting the residue at the corresponding position for inclusion in the sequence of said polypeptide sequence according to the corresponding residues given in Table 10.